Napari-OmniEM

Interactive electron microscopy analysis powered by foundation models.

Napari-OmniEM is a Napari plugin that provides a unified, GPU-accelerated interface for electron microscopy (EM) image processing. Built on top of EM-DINO and OmniEM, it enables scalable, high-quality inference across heterogeneous 2D and 3D EM datasets, bridging foundation models with practical, interactive EM workflows.

Napari-OmniEM supports both in-memory and on-disk (multi-GPU) inference, and task-aware model management, making it suitable for exploratory analysis, large-volume processing, and downstream quantitative studies.

Installation Getting Started Model Zoo

demo

TODO

  • [ ] support full-image inference in in-memory mode without sliding window processing.
  • [ ] share OmniEM models in memory across different solutions to reduce redundant memory usage.
  • EM-SSL Project: https://github.com/pku-maleilab/EM-SSL-project